Use import root to compile Protobuf files

[bilki]

This PR adds a new argument to the protoc argument list, that allows finding nested packages when multiple protobuf file imports come from different folders/modules.

It's a breaking change for skeuomorph users like mu-idlgen-sbt (if importRoot is mandatory, maybe it's a good idea to keep if Option[String] and provide a default None parameter?), that now have to instance a ProtoSource including a common root folder for all proto imports.

[pepegar]

LGTM!

[fedefernandez]

@bilki is this still mergeable?

[bilki]

It is, but there is another change in mu that needs to be merged too and then bump their dependency version on skeuomorph to the tag where we are going to release this change. Also this needs to be rebased against master.